Crystal structure of beta-2 glycoprotein I purified from plasma (PB2GPI)

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 41% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 7 copies
• BMA · beta-D-mannopyranose · sugar · 6 copies
• SO4 · Sulfate ion · ion · 13 copies · chains A
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 6V06 · Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI) · the same entry in another collection · chain A against A, TM-score 1.00
• P02749 · AlphaFold monomer V2.0 prediction for beta-2-glycoprotein 1 (P02749) · a predicted model of the same protein · chain A against A, TM-score 0.89

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P02749
• Elsewhere: RCSB PDB 6V06 · PDBe 6V06 · UniProt P02749